title: Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.
abstract: Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA.
authors.forename: Brandon K
authors.initials: BK
authors.lastname: Swan
authors.forename: Ben
authors.initials: B
authors.lastname: Tupper
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.forename: Federico M
authors.initials: FM
authors.lastname: Lauro
authors.forename: Manuel
authors.initials: M
authors.lastname: Martinez-Garcia
authors.forename: José M
authors.initials: JM
authors.lastname: González
authors.forename: Haiwei
authors.initials: H
authors.lastname: Luo
authors.forename: Jody J
authors.initials: JJ
authors.lastname: Wright
authors.forename: Zachary C
authors.initials: ZC
authors.lastname: Landry
authors.forename: Niels W
authors.initials: NW
authors.lastname: Hanson
authors.forename: Brian P
authors.initials: BP
authors.lastname: Thompson
authors.forename: Nicole J
authors.initials: NJ
authors.lastname: Poulton
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.forename: Silvia G
authors.initials: SG
authors.lastname: Acinas
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Giovannoni
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Moran
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cavicchioli
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D016680:Genome, Bacterial; D005843:Geography; D008386:Marine Biology; D009792:Oceans and Seas; D010933:Plankton / Q000145:classification* / Q000235:genetics; D014871:Water Microbiology
keywords: comparative genomics; marine microbiology; microbial ecology; microbial microevolution; operational taxonomic unit